5VGZ

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.

Lu, Y.Wu, J.Dong, Y.Chen, S.Sun, S.Ma, Y.B.Ouyang, Q.Finley, D.Kirschner, M.W.Mao, Y.

(2017) Mol Cell 67: 322-333.e6

  • DOI: 10.1016/j.molcel.2017.06.007
  • Primary Citation of Related Structures:  
    5VHF, 5VGZ, 5VHP, 5VHO, 5VHR, 5VHQ, 5VHS, 5VHH, 5VHJ, 5VHI

  • PubMed Abstract: 
  • The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP a ...

    The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9, and S5b. Using cryogenic electron microscopy, we analyzed the non-AAA structure of the p28-bound human RP at 4.5 Å resolution and determined seven distinct conformations of the Rpn1-p28-AAA subcomplex within the p28-bound RP at subnanometer resolutions. Remarkably, the p28-bound AAA ring does not form a channel in the free RP and spontaneously samples multiple "open" and "closed" topologies at the Rpt2-Rpt6 and Rpt3-Rpt4 interfaces. Our analysis suggests that p28 assists the proteolytic core particle to select a specific conformation of the ATPase ring for RP engagement and is released in a shoehorn-like fashion in the last step of the chaperone-mediated proteasome assembly.


    Organizational Affiliation

    State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China; Intel Parallel Computing Center for Structural Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: youdong_mao@dfci.harvard.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7A83Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
Find proteins for P35998 (Homo sapiens)
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PHAROS  P35998
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4B73Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
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PHAROS  P62191
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8C118Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
Find proteins for P62195 (Homo sapiens)
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PHAROS  P62195
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6BD107Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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PHAROS  P43686
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10BE104Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
Find proteins for P62333 (Homo sapiens)
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PHAROS  P62333
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AF115Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
Find proteins for P17980 (Homo sapiens)
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PHAROS  P17980
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1U935Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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PHAROS  Q99460
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3V488Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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PHAROS  O43242
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12W456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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PHAROS  O00232
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11X385Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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PHAROS  O00231
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6Y378Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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PHAROS  Q15008
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Entity ID: 12
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26S proteasome non-ATPase regulatory subunit 7Z286Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
Find proteins for P51665 (Homo sapiens)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13a374Homo sapiensMutation(s): 0 
Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens)
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PHAROS  Q9UNM6
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4b191Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
Find proteins for P55036 (Homo sapiens)
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PHAROS  P55036
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14c287Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
Find proteins for O00487 (Homo sapiens)
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PHAROS  O00487
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8d257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1e70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
Find proteins for P60896 (Homo sapiens)
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
c
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references